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Evans SE, Franks AE, Bergman ME, Sethna NS, Currie MA, Phillips MA. Plastid ancestors lacked a complete Entner-Doudoroff pathway, limiting plants to glycolysis and the pentose phosphate pathway. Nat Commun 2024; 15:1102. [PMID: 38321044 PMCID: PMC10847513 DOI: 10.1038/s41467-024-45384-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/20/2024] [Indexed: 02/08/2024] Open
Abstract
The Entner-Doudoroff (ED) pathway provides an alternative to glycolysis. It converts 6-phosphogluconate (6-PG) to glyceraldehyde-3-phosphate and pyruvate in two steps consisting of a dehydratase (EDD) and an aldolase (EDA). Here, we investigate its distribution and significance in higher plants and determine the ED pathway is restricted to prokaryotes due to the absence of EDD genes in eukaryotes. EDDs share a common origin with dihydroxy-acid dehydratases (DHADs) of the branched chain amino acid pathway (BCAA). Each dehydratase features strict substrate specificity. E. coli EDD dehydrates 6-PG to 2-keto-3-deoxy-6-phosphogluconate, while DHAD only dehydrates substrates from the BCAA pathway. Structural modeling identifies two divergent domains which account for their non-overlapping substrate affinities. Coupled enzyme assays confirm only EDD participates in the ED pathway. Plastid ancestors lacked EDD but transferred metabolically promiscuous EDA, which explains the absence of the ED pathway from the Viridiplantae and sporadic persistence of EDA genes across the plant kingdom.
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Affiliation(s)
- Sonia E Evans
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Anya E Franks
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Matthew E Bergman
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Nasha S Sethna
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Mark A Currie
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
- Department of Biology, University of Toronto-Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Michael A Phillips
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada.
- Department of Biology, University of Toronto-Mississauga, Mississauga, ON, L5L 1C6, Canada.
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Vera-Ruiz VA, Robinson J, Jermiin LS. A Likelihood-Ratio Test for Lumpability of Phylogenetic Data: Is the Markovian Property of an Evolutionary Process retained in Recoded DNA? Syst Biol 2021; 71:660-675. [PMID: 34498090 DOI: 10.1093/sysbio/syab074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 08/19/2021] [Accepted: 08/27/2021] [Indexed: 11/12/2022] Open
Abstract
In molecular phylogenetics, it is typically assumed that the evolutionary process for DNA can be approximated by independent and identically distributed Markovian processes at the variable sites and that these processes diverge over the edges of a rooted bifurcating tree. Sometimes the nucleotides are transformed from a 4-state alphabet to a 3- or 2-state alphabet by a procedure that is called recoding, lumping, or grouping of states. Here, we introduce a likelihood-ratio test for lumpability for DNA that has diverged under different Markovian conditions, which assesses the assumption that the Markovian property of the evolutionary process over each edge is retained after recoding of the nucleotides. The test is derived and validated numerically on simulated data. To demonstrate the insights that can be gained by using the test, we assessed two published data sets, one of mitochondrial DNA from a phylogenetic study of the ratites (Syst. Biol. 59:90-107 [2010]) and the other of nuclear DNA from a phylogenetic study of yeast (Mol. Biol. Evol. 21:1455-1458 [2004]). Our analysis of these data sets revealed that recoding of the DNA eliminated some of the compositional heterogeneity detected over the sequences. However, the Markovian property of the original evolutionary process was not retained by the recoding, leading to some significant distortions of edge lengths in reconstructed trees.
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Affiliation(s)
- Victor A Vera-Ruiz
- School of Mathematics and Statistics, University of Sydney, NSW 2006, Australia.,Department of Mathematics and Statistics, University of Nevada, Reno, NV 89557, USA
| | - John Robinson
- School of Mathematics and Statistics, University of Sydney, NSW 2006, Australia
| | - Lars S Jermiin
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia.,School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.,Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
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Hernandez AM, Ryan JF. Six-state Amino Acid Recoding is not an Effective Strategy to Offset Compositional Heterogeneity and Saturation in Phylogenetic Analyses. Syst Biol 2021; 70:1200-1212. [PMID: 33837789 PMCID: PMC8513762 DOI: 10.1093/sysbio/syab027] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 01/25/2023] Open
Abstract
Six-state amino acid recoding strategies are commonly applied to combat the effects of compositional heterogeneity and substitution saturation in phylogenetic analyses. While these methods have been endorsed from a theoretical perspective, their performance has never been extensively tested. Here, we test the effectiveness of six-state recoding approaches by comparing the performance of analyses on recoded and non-recoded data sets that have been simulated under gradients of compositional heterogeneity or saturation. In our simulation analyses, non-recoding approaches consistently outperform six-state recoding approaches. Our results suggest that six-state recoding strategies are not effective in the face of high saturation. Furthermore, while recoding strategies do buffer the effects of compositional heterogeneity, the loss of information that accompanies six-state recoding outweighs its benefits. In addition, we evaluate recoding schemes with 9, 12, 15, and 18 states and show that these consistently outperform six-state recoding. Our analyses of other recoding schemes suggest that under conditions of very high compositional heterogeneity, it may be advantageous to apply recoding using more than six states, but we caution that applying any recoding should include sufficient justification. Our results have important implications for the more than 90 published papers that have incorporated six-state recoding, many of which have significant bearing on relationships across the tree of life. [Compositional heterogeneity; Dayhoff 6-state recoding; S&R 6-state recoding; six-state amino acid recoding; substitution saturation.]
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Affiliation(s)
- Alexandra M Hernandez
- Whitney Laboratory for Marine Bioscience, 9505 Ocean Shore Boulevard, St. Augustine, FL, 32080, USA.,Department of Biology, University of Florida, 220 Bartram Hall, P.O. Box 118525, Gainesville, FL, 32611, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, 9505 Ocean Shore Boulevard, St. Augustine, FL, 32080, USA.,Department of Biology, University of Florida, 220 Bartram Hall, P.O. Box 118525, Gainesville, FL, 32611, USA
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Phillips JB, Ardell DH. Structural and Genetic Determinants of Convergence in the Drosophila tRNA Structure-Function Map. J Mol Evol 2021; 89:103-116. [PMID: 33528599 PMCID: PMC7884595 DOI: 10.1007/s00239-021-09995-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 01/11/2021] [Indexed: 10/29/2022]
Abstract
The evolution of tRNA multigene families remains poorly understood, exhibiting unusual phenomena such as functional conversions of tRNA genes through anticodon shift substitutions. We improved FlyBase tRNA gene annotations from twelve Drosophila species, incorporating previously identified ortholog sets to compare substitution rates across tRNA bodies at single-site and base-pair resolution. All rapidly evolving sites fell within the same metal ion-binding pocket that lies at the interface of the two major stacked helical domains. We applied our tRNA Structure-Function Mapper (tSFM) method independently to each Drosophila species and one outgroup species Musca domestica and found that, although predicted tRNA structure-function maps are generally highly conserved in flies, one tRNA Class-Informative Feature (CIF) within the rapidly evolving ion-binding pocket-Cytosine 17 (C17), ancestrally informative for lysylation identity-independently gained asparaginylation identity and substituted in parallel across tRNAAsn paralogs at least once, possibly multiple times, during evolution of the genus. In D. melanogaster, most tRNALys and tRNAAsn genes are co-arrayed in one large heterologous gene cluster, suggesting that heterologous gene conversion as well as structural similarities of tRNA-binding interfaces in the closely related asparaginyl-tRNA synthetase (AsnRS) and lysyl-tRNA synthetase (LysRS) proteins may have played a role in these changes. A previously identified Asn-to-Lys anticodon shift substitution in D. ananassae may have arisen to compensate for the convergent and parallel gains of C17 in tRNAAsn paralogs in that lineage. Our results underscore the functional and evolutionary relevance of our tRNA structure-function map predictions and illuminate multiple genomic and structural factors contributing to rapid, parallel and compensatory evolution of tRNA multigene families.
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Affiliation(s)
- Julie Baker Phillips
- Quantitative and Systems Biology Program, University of California, Merced, CA, 95343, USA
- Department of Biology, Cumberland University, 1 Cumberland Square, Lebanon, TN, 37087, USA
| | - David H Ardell
- Quantitative and Systems Biology Program, University of California, Merced, CA, 95343, USA.
- Department of Molecular and Cell Biology, University of California, Merced, CA, 95343, USA.
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